title: EpCAM, GFPpos, 9

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

institute: Consiglio Nazionale delle Ricerche

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore (options: "--quality 20 --length 25")
Trimmed reads were mapped to GRCh38 whole genome using STAR v2.7.6a (options: "--outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10")
Gene counts of mapped reads were obtained with the Subread package ("featureCounts" function with options: "-g gene_name -s 0")
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include counts of mapped reads for each Sample

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMART-Seq v4 for mRNA-seq (TaKaRa) Library Prep Kit following manufacturer's protocols.

value: Liver

tag: group

value: GFPpos

tag: cell type

value: Cholangiocytes

value: WT

value: Lentiviral vector (LV) administration at post-natal day 1


title: F_8Gy_Day3_25y

status: Public on May 11 2024

type: protein

city: Rockville

first: Yu

last: Fan

state: MD

address: 9609 Medical Center Dr

country: USA

institute: NCI/CBIIT

hyb_protocol: A SOMAmer-protein binding step is followed by a series of partitioning and wash steps to convert relative epitope concentrations into measurable nucleic acid signals that are quantified using DNA-hybridization microarrays

scan_protocol: The cyanine-3 signal from the SOMAmer reagent is detected on microarrays

data_processing: Intraplate and interplate variations were adjusted by SOMAscan® v4 Data Standardization pipeline. Log2(data +1) transformation was performed before all downstream analysis.

label: biotin

molecule: protein

organism: Mus musculus

source_name: plasma collected after irradiation

label_protocol: SOMAmer® (Slow Off-rate Modified Aptamer) reagents which consist of short single-stranded DNA sequences that incorporate hydrophobic modifications

growth_protocol: nine to eleven week old female or male C57BL6 mice received a single total body irradiation (TBI) dose of 2, 4, or 8 Gy or sham radiation.  All mice receiving TBI were confined unanesthetized in plexiglass containers.  All animal studies were conducted in accordance with the principles and procedures outlined in the NIH Guide for the Care and Use of Animals and procedures were approved by the NIH Lab Animal Safety Program under an approved protocol #ROB170.

extract_protocol: Approximately 140ul of plasma per sample was used for the Somalogic SomaScan Assay

treatment_protocol: Murine in vivo models utilized a Precision X-ray source at a dose rate of 407 cGy/min. Dose rate was calibrated based upon the procedures described in American Association of Physicist in Medicine (AAPM) Task Group Report 61 (TG-61) with regard to the following conditions:  X-ray tube potential was 320 kV, half value layer (HVL) is 0.8 mm Copper (Cu), source to surface distance (SSD) was 50 cm.  Dose rate was measured at 2 cm depth in solid water phantom using a PTW model: N23342 ion chamber and Inovision, model 35040 electrometer.

tag: strain

tag: tissue

value: plasma

tag: gender

value: F

tag: dose

tag: timepoint


title: F_8Gy_Day1_24y


title: Day_1_FSHD2_3_R1

type: SRA

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences 3

institute: UC Irvine

library_source: transcriptomic

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were mapped to hg38 by STAR (version 2.5.1b) using defaults except with a maximum of 10 mismatches per pair, a ratio of mismatches to read length of 0.07, and a maximum of 10 multiple alignments.
Quantitation was performed using RSEM (version 1.2.31) with defaults with gene annotations for protein coding genes and lncRNAs from GENCODE v28. Results were output as counts, and effective gene length was used after normalization to compute transcripts per million (TPM).
Counts were batch corrected for the two different library prep methods using ComBat-seq from sva (version 3.36.0).
Genes were filtered for 10 counts in all samples of at least one condition (same FSHD status, muscle group and differentiation day) using filterByExpr from edgeR (version 3.30.3).
Genome_build: hg38
Supplementary_files_format_and_content: RSEM output tab-delimited text files with abundance measures in counts and TPM.

molecule: polyA RNA

organism: Homo sapiens

source_name: Primary myoblasts from quadricep biopsy

extract_protocol:
Cells were lifted using trypsin. Total RNA was extracted by using the RNeasy kit (QIAGEN).
RNA was converted to cDNA using the Smart-Seq 2 protocol (Picelli, et al., Nat. Protoc., 2014). Libraries were constructed with the Nextera DNA Library Prep Kit (Illumina) for days 0 to 5 for FSHD2-3. The Nextera DNA Flex Library Prep Kit (Illumina) was used for all other RNA-seq samples. Libraries were sequenced on the Illumina NextSeq500 with paired-end 43 bp reads to a depth of 5 to 40 million reads.

tag: cell line

tag: day of differentiation

value: Day 1

tag: fshd status

tag: muscle source

value: quadricep

tag: library prep kit

value: Nextera DNA Library Prep Kit (FC-121-1030, Illumina)


title: EpCAM, GFPneg, 9

country: Italy

molecule: total RNA

value: GFPneg

tag: genotype

tag: treatment


title: 207760740001_R12C01

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

description: pancreas

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human primary cell DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).


title: F_8Gy_Day1_23y


title: Day_0_FSHD2_3_R2

value: Day 0


title: 207760740001_R08C01

description: pancreas


title: F_8Gy_Day1_22y


title: EpCAM, GFPpos, 8


title: 207760740001_R10C01

description: pancreas


title: EpCAM, GFPneg, 8


title: 207760740001_R04C01

description: skin


title: 207760740001_R14C01

description: pancreas


title: EpCAM, GFPpos, 4


title: Day_5_FSHD2_4_R2

value: Day 5

value: Nextera DNA Flex Library Prep Kit (20018704, Illumina)


title: 207760740001_R05C02

description: colon


title: 207760740001_R11C01

description: Illumina Control DNA

source_name: Human cell line DNA


title: F_8Gy_Day1_20y


title: 207760740001_R15C01

description: Illumina Control DNA


title: EpCAM, GFPneg, 4


title: 207760740001_R02C01

description: skin


title: 207760740001_R13C01

description: Illumina Control DNA


title: Day_5_FSHD2_4_R1


title: F_8Gy_Day1_21y


title: 207760740001_R07C01

description: skin


title: 207760740001_R03C01

description: skin


title: 207760740001_R13C02

description: NK cells


title: 207760740037_R14C03

description: LNCaP


title: 207760740001_R06C01

description: pancreas


title: Day_4_FSHD2_4_R2

value: Day 4


title: F_4Gy_Day7_54y


title: Day_4_FSHD2_4_R1


title: EpCAM, GFPpos, 3


title: 207760740037_R16C03

description: skin


title: EpCAM, GFPneg, 3


title: 207760740037_R10C03

description: LNCaP


title: Day_3_FSHD2_4_R2

value: Day 3


title: 207760740001_R01C01

description: skin


title: Day_3_FSHD2_4_R1


title: EpCAM, GFPneg, 2


title: 207760740037_R08C03


title: 207760740037_R06C03


title: F_4Gy_Day7_52y


title: Day_2_FSHD2_4_R2

value: Day 2


title: 207760740001_R09C01

description: Illumina Control DNA


title: 207760740037_R12C03

description: LNCaP


title: F_4Gy_Day7_53y


title: EpCAM, ConfettiPos, 6

value: Liver

value: ConfettiPo

value: Tamoxifen post-natal day 1


title: F_4Gy_Day7_51y


title: 207760740001_R05C01

description: CD8+ T cells


title: 207760740037_R02C03


title: EpCAM, ConfettiPos, 5

value: Cholangiocytes


title: Day_1_FSHD2_4_R2


title: F_4Gy_Day7_49y


title: 207760740037_R04C03


title: 207760740037_R15C03


title: F_4Gy_Day7_50y


title: Day_1_FSHD2_4_R1


title: F_4Gy_Day3_48y


title: Day_2_FSHD2_4_R1


title: EpCAM, GFPpos, 2

value: GFPpos

value: WT

value: Lentiviral vector (LV) administration at post-natal day 1


title: Day_0_FSHD2_4_R2


title: EpCAM, ConfettiPos, 3


title: EpCAM, ConfettiPos, 2


title: Day_0_FSHD2_4_R1


title: 207760740037_R11C03

description: Human blood standard 0


title: EpCAM, ConfettiPos, 4


title: F_4Gy_Day3_46y

value: plasma

value: F


title: F_4Gy_Day3_47y


title: 207760740037_R13C03


title: EpCAM, ConfettiPos, 1


title: F_4Gy_Day3_45y


title: EpCAM, ConfettiNeg, 6

value: ConfettiNeg


title: Day_12_Control_4_R1

value: Day 12

value: Control

value: quadricep


title: F_8Gy_Day1_19y


title: EpCAM, ConfettiNeg, 5


title: 207760740037_R09C03

description: Human blood standard 50


title: 207760740037_R07C03

description: Human blood standard 100


title: Day_12_Control_3_R2

value: Nextera DNA Flex Library Prep Kit (20018704, Illumina)


title: Day_12_Control_4_R2


title: F_4Gy_Day3_44y


title: Day_0_FSHD2_3_R1

value: Day 0

value: Nextera DNA Library Prep Kit (FC-121-1030, Illumina)


title: EpCAM, ConfettiNeg, 4


title: F_4Gy_Day3_43y


title: Day_12_Control_3_R1


title: EpCAM, ConfettiNeg, 3


title: Day_12_FSHD2_4_R2


title: F_4Gy_Day1_42y


title: Day_12_FSHD2_4_R1


title: F_4Gy_Day1_40y


title: EpCAM, ConfettiNeg, 2


title: Day_12_FSHD2_3_R1


title: F_4Gy_Day1_41y


title: EpCAM, ConfettiNeg, 1


title: Day_12_FSHD2_3_R2


title: F_4Gy_Day1_39y


title: 207760740037_R03C03

description: Jurkat standard 50


title: iPSC-derived fibroblasts, donor 2, 8h post irradiation

city: montreal

first: Christian

last: Beausejour

state: Québec

address: 3175 Cote Ste-Catherine

department: Pharmacologie et physiologie

country: Canada

institute: Université de Montréal

data_processing:
Reads were trimmed using trimmomatic v0.39, aligned to the human genome GRCh38 using STAR2.7.9 and quantified using RSEM 1.3.1.
Assembly: GRCh38
Supplementary files format and content: Results fastQ

growth_protocol: i-HF were cultured similarly to HF with DMEM 10% FBS +1% penicillin/streptomycin, apart from being plated on 1% Geltrex-coated plates to prevent cell death during the early expansion phase. Throughout all culture steps, cells were maintained at a normoxic (5%) oxygen level.

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen). RNA quality control, library preparation and sequencing were performed by the Gé-nome Québec platform. RNA quality was assessed using the Perkin Elmer LabChip (RIN > 6.5).
Illumina Stranded mRNA Prep was used for library preparation.

treatment_protocol: 15 Gy irradiation

value: iPSC-d fibroblasts

value: Irradiation


title: 207760740037_R05C03

description: Jurkat standard 0


title: Fibroblasts, donor 2, control

value: Fibroblasts


title: F_4Gy_Day1_38y


title: 207760740037_R01C03

description: Jurkat standard 100


title: Day_12_FSHD2_1_R2

source_name: Primary myoblasts from tibialis anterior biopsy

value: tibialis anterior


title: Day_12_FSHD2_1_R1


title: 207760740037_R16C02

description: EpigenDx standard_100


title: iPSC-derived fibroblasts, donor 1, 8h post irradiation


title: Day_12_FSHD2_2_R2


title: F_4Gy_Day1_37y


title: F_2Gy_Day7_17y


title: F_2Gy_Day7_18y


title: iPSC-derived fibroblasts, donor 3, 8h post irradiation


title: Day_12_FSHD2_2_R1


title: Fibroblasts, donor 3, 8h post-irradiation


title: Day_12_Control_1_R2


title: F_2Gy_Day7_16y


title: F_2Gy_Day7_15y


title: Fibroblasts, donor 2, 8h post-irradiation


title: 207760740037_R10C02

description: EpigenDx standard_25


title: 207760740037_R12C02

description: EpigenDx standard_50


title: 207760740037_R14C02

description: EpigenDx standard_75


title: 207760740037_R08C02

description: EpigenDx standard_10


title: 207760740037_R06C02

description: EpigenDx standard_5


title: Day_12_Control_1_R1


title: iPSC-derived fibroblasts, donor 2, control


title: Day_12_Control_2_R2


title: Fibroblasts, donor 3, control


title: F_2Gy_Day7_14y


title: F_2Gy_Day7_13y


title: F_2Gy_Day3_12y


title: Day_12_Control_2_R1


title: 207760740037_R13C02

description: LNCaP


title: F_2Gy_Day3_11y


title: 207760740037_R11C02


title: iPSC-derived fibroblasts, donor 1, control


title: Control_replicate_8

city: Basel

first: Gennaro

last: De Libero

address: Hebelstrasse 20

department: Dept of Biomedicine

country: Switzerland

institute: University of Basel

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library unscreened replicate 8

library_source: genomic

data_processing:
Library strategy: PCR Amplicon Sequencing
reads trimmed to guide seqence using Trimmomatic version 0.36
Trimmed reads aligned to index prepared fromGecKO v2 guide RNA sequences using Bowtie version 2.2.9
Raw counts analysed using edgeR version 3.24
Genome_build: Not applicable
Supplementary_files_format_and_content: raw counts

source_name: A375 cultured cells

growth_protocol: A375-MR1-Cas9 cell were grown at 37C in RPMI-1640 supplemented with 10% fetal calf serum, 2mM L-Glutamine, 1 mM Sodium Pyruvate, 1x non-essential amino acids, and 50 ug/mL Kanamycin

extract_protocol:
gDNA purification from cultured cells using Macharey Nagel NucleoSpin Tissue kit
PCR from gDNA and indexing using Nextera indexes following protocol of Shalem et al (2014) and standard Illumina protocols

treatment_protocol: TC5A87 treated replicates underwent 4 consecutive rounds of killing at an E:T of 2:1 afterwhich they were allowed to recover for 24 hrs before harvesting for gDNA extraction. Control replicates were harvested after 96 hours of puromycin selection.

value: control


title: Fibroblasts, donor 1, 8h post-irradiation


title: iPSC-derived fibroblasts, donor 3, control


title: F_2Gy_Day3_10y


title: 207760740037_R02C02

description: LNCaP


title: Control_replicate_7

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library unscreened replicate 7


title: Control_replicate_6

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library unscreened replicate 6


title: F_2Gy_Day3_9y


title: 207760740037_R03C02


title: 207760740037_R05C02


title: Control_replicate_5

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library unscreened replicate 5


title: 207760740037_R04C02

description: EpigenDx standard 0


title: F_2Gy_Day3_8y


title: 24hr MVA infected Hi-C Bio rep 2

city: Los Alamos

first: Christina

middle: Rene

last: Steadman

state: New Mexico

address: Bikini Atoll Rd

department: Earth & Environmental Sciences Division

institute: Los Alamos National Laboratory

description: Processed .hic files were merged across biological replicates. Therefore, single merged.hic file represents both replicates

data_processing:
Hi-C paired fastq.gz files from paired-end Illumina sequencing were analyzed using the JuicerHi-C pipeline. Samples were aligned to Chlorocebus sabaeus reference genome (GCF_000409795.2_Chlorocebus_sabeus_1.1_genomic.fasta)downloaded from the NCBI genome browser. Prior to alignment, the reference fasta file wasmodified to include the sequence of the Vaccina virus (Accession No. U94848, downloadedfrom GenBank). Restriction sites associated with the Arima protocol (used to construct Hi-C libraries) were identified using Juicer.
Assembly: The Chlorocebus sabaeus reference genome (GCF_000409795.2) appended with the vaccinia virus (VACV) genome, retrieved from GenBank (U94848.1)
Supplementary files format and content: Hi-C files (.hic) were constructed using default settings within Juicer, and for subsequent analysis, the mapping quality threshold of ‘q = 30’ was used. The spectral statistic was utilized
Supplementary files format and content: The spectral statistic was utilized to measure reproducibility between Hi-C replicates. The Hi-C replicates demonstrated broad biological reproducibility as demonstrated by this statistic (median scores >0.75). Replicate Hi-C maps were merged using the “mega” function in Juicer.

organism: Chlorocebus sabaeus

source_name: Kidney derived cell line

growth_protocol: Cryopreserved Vero cells, derived from the kidney tissue of a normal adult African greenmonkey, were sourced from the ATCC (Cat # CCL-81). Cells were thawed, passaged, expanded,and seeded for viral infection in complete medium consisting of Dulbecco’s Modified Eagle’sMedium (DMEM) containing 4 mM L-Glutamine (ATCC, Cat # 30-2002), supplemented with10% (v/v) Fetal Bovine Serum (FBS, ATCC, Cat # 30-2020) and filter-sterilized beforeuse. Vero cells were maintained at 37°C with 5% CO2 and 95% relative humidity. Vero cellswere cryopreserved at passage #7 from the original source vial using freeze medium consistingof DMEM supplemented with 10% (v/v) FBS and 5% (v/v) dimethylsulfoxide (DMSO, ATCC,Cat # 4-X).

extract_protocol:
Cells were harvested in two biological replicates (A and B) per condition (mock-infected andMVA-infected) at each timepoint (12 hrs, 18 hrs, and 24 hrs post-infection). At each timepoint,cells were washed using 1X phosphate-buffered saline (PBS, Gibco, Cat # 10010049), detachedfor 15 min at 37°C using 1X TrypLE Express Enzyme (Gibco, Cat # 12604021), andresuspended in pre-warmed complete medium before cell counting with the Scepter 3.0Handheld Cell Counter and 60 μm Counter Sensors. At each timepoint, mock-infected andMVA-infected cell suspensions were divided and processed for Hi-C, ATAC-seq and RNA-seqtechniques
For Hi-C, 1x10^6 cells per aliquot were processed in triplicate on the day of cell harvest. Cellswere resuspended in 1X PBS and cross-linked for exactly 10 min using 37% (w/v) formaldehydecontaining 10-15% (v/v) methanol (Sigma, Cat # 252549) at a final concentration of 2%(v/v). Formaldehyde was quenched for 5 min using glycine at a final concentration of 0.2M. Cross-linked cells were incubated on ice for an additional 15 min, then pelleted bycentrifugation and washed in 1X PBS. Washed cells were pelleted by centrifugation, and the drypellets were snap-frozen on dry ice for long-term storage. These cross-linked cells weresubsequently processed for Hi-C analysis per the Arima Hi-C Kit manual (Cat # A160134) usingthe reagents provided in the kit. In summary, cross-linked cells were lysed and enzymaticallytreated to create proximally-ligated DNA, which was then purified via AMPure XP Reagent(Beckman, Cat # A63880). This proximally-ligated DNA was used to create DNA libraries for sequencing per the Arima Hi-C Library Preparation user guide (Cat # A160141). DNA librarieswere then sequenced via the Illumina NextSeq 2000 sequencer platform at the Los AlamosNational Laboratory Genome Center.

treatment_protocol: Cryopreserved Vero cells were thawed at passage #8 and propagated for 2 passages prior toseeding for viral infection. At the time of seeding, a cell suspension was made in pre-warmedcomplete medium and digitally counted using the Scepter 3.0 Handheld Cell Counter and 60 μmCounter Sensors (Millipore, Cat # PHCC360KIT). Cells were seeded for viral infection atpassage #11 into replicate tissue culture flasks and multi-well plates using 5x10^6 cells per T175flask or 5x10^5 cells per well in 12-well plates. Seeded flasks and plates were incubated for 24 hrsat 37°C, yielding ~1x10^7 cells per flask and ~1x10^6 cells per well at the time of infection. Modified Vaccinia Ankara virus, strain VACV-MVA, was obtained from the ATCC (Cat # VR-1508). VACV-MVA viral stock was diluted in infection medium consisting of DMEMsupplemented with 2% (v/v) FBS. Vero cells were infected at 0 hrs using 0.4 MOI in a minimalvolume of inoculum (3 mL per flask) for 1 hr at 37°C; 17 mL infection medium was added priorto incubation for 12-24 hrs at 37°C. In parallel to the flasks, 12-well plates for ICC staining andcell imaging were also infected in parallel to the flasks at 0 hr using 0.4 MOI in 300 μL per well;then 700 μL infection medium was added prior to incubation for 12-24 hrs at 37°C.

value: Kidney derived cell line

value: Vero CCL-81

value: 24hr MVA infected


title: Control_replicate_4

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library unscreened replicate 4


title: 24hr Mock infected Hi-C Bio rep 2

value: 24hr Mock infected


title: 207760740037_R09C02


title: 207760740037_R15C02

description: LNCaP


title: Control_replicate_3

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library unscreened replicate 3


title: 207760740037_R07C02


title: 24hr Mock infected Hi-C Bio rep 1


title: F_2Gy_Day1_6y

value: plasma

value: F


title: F_2Gy_Day3_7y


title: 207760740037_R16C01


title: 18hr MVA infected Hi-C Bio rep 2

value: 18hr MVA infected


title: Control_replicate_2

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library unscreened replicate 2


title: 207760740037_R01C02


title: Control_replicate_1

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library unscreened replicate 1


title: 18hr MVA infected Hi-C Bio rep 1


title: F_2Gy_Day1_4y


title: TC5A87_replicate_8

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library screened by TC5A87 MR1-restricted T cell clone replicate 8


title: 18hr Mock infected Hi-C Bio rep 2

value: 18hr Mock infected


title: 207760740037_R14C01


title: 207760740037_R12C01


title: F_2Gy_Day1_3y


title: 18hr Mock infected Hi-C Bio rep 1


title: TC5A87_replicate_6

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library screened by TC5A87 MR1-restricted T cell clone replicate 6


title: TC5A87_replicate_5

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library screened by TC5A87 MR1-restricted T cell clone replicate 5


title: F_2Gy_Day1_1y


title: 12hr MVA infected Hi-C Bio rep 2

value: 12hr MVA infected


title: F_2Gy_Day1_2y


title: 12hr MVA infected Hi-C Bio rep 1


title: 207760740037_R08C01

description: LNCaP


title: 207760740037_R06C01

description: LNCaP


title: 207760740037_R10C01

description: LNCaP


title: 12hr Mock infected Hi-C Bio rep 2

value: 12hr Mock infected


title: TC5A87_replicate_3

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library screened by TC5A87 MR1-restricted T cell clone replicate 3


title: TC5A87_replicate_4

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library screened by TC5A87 MR1-restricted T cell clone replicate 4


title: 12hr Mock infected Hi-C Bio rep 1


title: TC5A87_replicate_2

description: A375-MR1-Cas9 expressing cells transfected with GecKO v2 library screened by TC5A87 MR1-restricted T cell clone replicate 2


title: 207760740037_R04C01


title: △J/△J-like

status: Public on May 10 2024

city: Hangzhou

first: Kaiying

last: Cheng

state: Zhejiang

address: No.2318, Yuhangtang Rd

department: Department of Immunology and Pathogen Biology

country: China

institute: Hangzhou Normal University

data_processing:
filtering the raw data
sequencing error rate checks
examining GC content distribution
quantifying gene expression
Differential expression analysis
Assembly: ASM163882v1
Supplementary files format and content: The file “gene_count” includes the raw read count values for each sample.
Supplementary files format and content: The file “gene_fpkm” includes the FPKM values for each sample.

organism: Deinococcus radiodurans

source_name: Deinococcus radiodurans R1

extract_protocol:
Wild-type and mutant cells were cultured until reaching an OD600 of 0.8. They were then centrifuged and resuspended in PBS buffer at pH 7.0. Total RNA was extracted from two independent biological replicates for each group using the TRIzol method following the manufacturer's protocol (Ambion, Foster City, CA, United States). RNA quality, including degradation and contamination, was assessed by electrophoresis on 1% agarose gels. Additionally, RNA integrity was evaluated using the RNA Nano 6000 Assay Kit on the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The transcriptome Library preparation, clustering and sequencing were performed by Novogene Corporation (Beijing, China). Two micrograms of RNA per sample was used as the input material for library preparation, and then, a Ribo-ZeroTM Magnetic Kit (Epibio, MRZB12424) was used to remove rRNA. Subsequently, the obtained mRNA is randomly fragmented using divalent cations in the Fragmentation Buffer. Using the fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA is synthesized in the presence of MMuLV reverse transcriptase (NEB, USA). Then, the RNA strand is degraded with RNase H (NEB, USA), and the second strand of cDNA is synthesized using dUTP instead of dTTP as the raw material in the presence of DNA polymerase I. The purified double-stranded cDNA undergoes end repair, adenylation, and adapter ligation. USER enzyme (NEB, USA) is then added to degrade the second cDNA strand containing uracil (U). The cDNA fragments of approximately 370-420 bp are size-selected using AMPure XP beads, followed by PCR amplification. The PCR products are purified again using AMPure XP beads to obtain the final library.

value: Deinococcus radiodurans R1

value: drrecj/drrecj-like double deletion


title: T24-KO-M1 cells (IP)

type: RNA

city: Guangzhou

first: Ying

last: Xiaoling

address: 250 Changgang east road, Guangzhou

institute: The second affiliated Hospital of Guangzhou Medical University

description: Raw data file: T24-KO-M1.txt

hyb_protocol: The labeled RNAs were combined together and hybridized onto Arraystar Human small RNA Microarray (8x15K, Arraystar)

scan_protocol: After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.
Differentially m7G-methylated RNAs between two comparison groups were identified by fold change (FC) and statistical significance (p-value) thresholds

source_name: METTL1-knockout bladder cancer cells

label_protocol: The “IP” and “Sup” RNAs were enzymatically labeled with Cy5 and Cy3 respectively

growth_protocol: cells were kept in 10% FBS 1640

extract_protocol: The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions, 1-5 μg of each total RNA sample was immunoprecipitated by 6 μg anti-m7G antibody

value: Bladder Cancer cells

tag: rip antibody

value: anti-m7G antibody

tag: fraction

value: m7G-IP RNA


title: 207760740037_R02C01


title: △J

value: drrecj deletion


title: △J-like

value: drrecj-like deletion


title: S2-UPF1KD-2

city: Birmingham

first: Matthew

last: Wright

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: instrument model: Illumina NovaSeq X Plus

data_processing:
Sequences trimmed using TRIMMOMATIC PE
Sequences aligned to Dm6.56 using HISAT2
SAMtools to sort and convert sam files to BAM files
HTSeq to calculate raw counts from bam files
DESeq2 for differential expression analysis
Assembly: Dm6.56 FlyBase (https://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.56_FB2024_01/)
Supplementary files format and content: Raw gene counts in plain .txt files, annotated with FlyBase Gene ID

organism: Drosophila melanogaster

source_name: S2 cell

growth_protocol: Cells grown at 27 degrees celcius, in Schneider's Insect Cell Media, supplemented with Fetal Bovine Serum and antibotics (Penicillin and Streptomycin)

extract_protocol:
RNA was extracted using TRIzol. The upper phase was taken, and RNA was precipitated. Precpitated RNA was dissolved in dH2O.
Library was constructed by Novogene, following polyA enrichment

value: S2 cell


title: WT

value: WT


title: S2-WT-2


title: T24-KO-M1 cells (Sup)

description: Raw data file: T24-KO-M1.txt

value: Sup RNA


title: S2-UPF1KD-1


title: T24 cells (IP)

description: Raw data file: T24.txt

source_name: Bladder Cancer cells

value: control


title: 207760740037_R15C01


title: F_2Gy_Day1_5y

value: plasma


title: S2-WT-1


title: T24 cells (Sup)

description: Raw data file: T24.txt


title: RNAseq_Ilus_rep2

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Bisulfite-seq: Methylpy (Schultz et al., 2015) with Cutadapt v1.9 and Bowtie 2.2.4.
RNA-seq: Trimmomatic v0.33 for filtering reads and Kallisto v0.50.0 for mapping
Assembly: Tair10 for Arabidopsis thaliana
Assembly: RS08 for Raphanus raphanistrum (https://ngdc.cncb.ac.cn/gwh/Assembly/9805/show)
Assembly: ASM90040641v1 assembly for I. lusitanica (PRJEB26555 in EBI)
Supplementary files format and content: compressed tab-separated text files in allc format. "allc" stands for all cytosine (C). Each row in an allc file corresponds to one cytosine in the genome. An allc file contain 7 mandatory columns and no header (https://github.com/yupenghe/methylpy#output-format).
Supplementary files format and content: raw count files including target_id, length, eff_length, est_counts, and tpm for RNA-seq data.

organism: Isatis lusitanica

source_name: leaf

growth_protocol: Plants were grown at 23C under 15 hours of day light condition.

extract_protocol:
genomic DNA was isolated from leaf tissues using the DNeasy Plant Mini Kit (Qiagen), RNA was isolated from leaf tissues using the Qiagen Plant Mini Kit
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al., 2015). Briefly, genomic DNA was sonicated to around 200 bp using a Covaris S-series focused ultrasonicator, and end-repaired with an End-It DNA end-repair kit (Epicentre). The end-repaired DNA was subjected to A-tailing using Klenow 3′–5′ exo− (NEB) and ligated to methylated adapters using T4 DNA ligase (NEB). The ligated DNA was treated with sodium bisulfite reagent using the EZ DNA methylation-Gold kit and amplified using KAPA HiFi uracil + Readymix Polymerase. RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina) following the manufacturer’s instructions with limited modifications.

value: leaf


title: RNAseq_Ilus_rep1


title: MethylC-seq_I_lusitanica


title: RNAseq_Rra_rep3

organism: Raphanus raphanistrum


title: 207760740037_R11C01


title: MethylC-seq_R_raphanistrum


title: RNAseq_Rra_rep1


title: RNAseq_Rra_rep2


title: 207760740037_R13C01


title: RNAseq_Ilus_rep3


title: 24hr MVA infected Hi-C Bio rep 1

value: Kidney derived cell line

value: Vero CCL-81

value: 24hr MVA infected


title: Fibroblasts, donor 1, control

value: Fibroblasts


title: Vagal sensory neurons-M

city: bronx

first: Young-Hwan

last: Jo

state: NY

address: 1300 Morris Park ave, Forchheimer 505B

institute: Albert Einstein college of Medicine

library_source: transcriptomic single cell

data_processing:
The libraries were sequenced with ~200 million PE150 reads per sample on Illumina NovaSeq. The raw sequencing reads were analyzed with the mouse reference genome (mm10) with theaddition of the human growth hormone poly(A) (hgGH-poly(A)) transgene sequence found in AAVrg-CreusingCell Ranger v7.1.0. Introns were included in the analyses.To further clean the data,Debris Identification using the Expectation Maximization(DIEM) program was usedto filter the barcodes (from raw_feature_bc_matrix of each sample), keeping barcodes with debris scores < 0.5, number of features (genes) > 250, and UMI count > 1000.
The cellranger reanalyze function was used to analyze the samples with only the filtered, barcodes. The UMAP was generated by the cellranger reanalyze function, running at the default setting.
Differential gene expression was determined using the 10x Genomics Loupe Browser.
Assembly: mm10
Supplementary files format and content: cloupe file and gene expression

source_name: Vagus nerve ganglion

extract_protocol:
Thirty vagus nerve ganglia were collected from eight male and seven female Rosa26-eGFPf  mice injected with AAVrg-Cre into the liver four weeks after viral injection.16 vagus nerve ganglia from males and 14 vagus nerve ganglia from females were flash-frozen. Individual tissue samples were divided into separate pools for males and females. These pooled samples were subsequently homogenized and lysed using Triton X-100 in RNase-free water to isolate the nuclei. For nuclear isolation, we followed the 10x genomics protocol, CG000124 (Rev. F).
The isolated nuclei were diluted to 700 nuclei/µl for standardized 10x capture. The 10x Genomics single cell protocol was immediately proceeded using 10x Genomics Chromium Next GEM 3' Single Cell Reagent kits v3.1.
Single nucelus RNA sequencing

value: Vagus nerve ganglion

tag: Sex

value: male

tag: diet

value: standard chow diet


title: 207760740037_R07C01

description: Illumina Control DNA


title: Vagal sensory neurons-F

value: Female


title: 207760740037_R09C01


title: 207760740037_R05C01

description: Illumina Control DNA


title: DO560_M_23_Liver_GT19-33677

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.  counts_matrix.csv: raw counts quantified by EMASE and processed by/RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.  vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.  mrna_annots.csv: gene annotation file ENSEMBL version 75.
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

source_name: liver

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step.
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

treatment_protocol: Diversity Outbred mice were sensitized on a high-fat, high-sugar (HFHS) diet

value: liver

value: 45percent  fat


title: DO375_M_21_Liver_GT19_33753


title: DO147_F_18_Liver_GT19_33751


title: DO247_F_19_Liver_GT19_33628


title: DO559_M_23_Liver_GT19-33739


title: bone marrow_untreatment_SLE_R1

city: Fuzhou city

first: He

last: Juanjuan

address: East Street, Gulou District,

institute: Fujian Provincial Hospital

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified using fold change cutoff or through Volcano Plot filtering respectively. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated in detail with the circRNA/miRNA interaction information.

source_name: bone marrow,untreatment,SLE,R1

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enrich circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Bone marrow samples from SLE patients and normal human.

extract_protocol: The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1000 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: The bone marrow samples were collected and stored in test tubes at 4℃, and the samples were processed within 12 h.

tag: disease

value: healthy

value: bone marrow

value: female

tag: age


title: bone marrow_untreatment_NOR_R3

source_name: bone marrow,untreatment,NOR,R3

value: SLE

tag: tissue


title: bone marrow_untreatment_SLE_R2

source_name: bone marrow,untreatment,SLE,R2


title: DO557_M_23_Liver_GT19_33586


title: DO558_M_23_Liver_GT19-33521


title: DO391_M_21_Liver_GT19_33752


title: bone marrow_untreatment_NOR_R2

source_name: bone marrow,untreatment,NOR,R2


title: DO556_M_23_Liver_GT19_33312


title: DO554_M_23_Liver_GT19_33575


title: DO555_M_23_Liver_GT19_33423


title: DO552_M_23_Liver_GT19-33664


title: DO551_M_23_Liver_GT19-33709


title: bone marrow_untreatment_NOR_R1

source_name: bone marrow,untreatment,NOR,R1


title: DO553_M_23_Liver_GT19_33568


title: DO549_M_23_Liver_GT19_33458


title: DO550_M_23_Liver_GT19_33314


title: DO548_M_23_Liver_GT19_33387


title: DO544_M_23_Liver_GT19-33672


title: DO547_M_23_Liver_GT19_33357


title: DO545_M_23_Liver_GT19_33335


title: 207760740037_R01C01

description: Illumina Control DNA


title: 207760740037_R03C01

description: Illumina Control DNA


title: DO543_M_23_Liver_GT19-33689


title: DO541_M_23_Liver_GT19_33315


title: DO535_M_23_Liver_GT19_33302


title: DO542_M_23_Liver_GT19_33320


title: DO540_M_23_Liver_GT19_33362


title: DO531_M_23_Liver_GT19-33530


title: DO539_M_23_Liver_GT19-33633


title: DO536_M_23_Liver_GT19-33545


title: DO533_M_23_Liver_GT19-33653


title: DO537_M_23_Liver_GT19_33299


title: DO534_M_23_Liver_GT19-33723


title: DO530_M_23_Liver_GT19-33682


title: DO532_M_23_Liver_GT19-33515


title: DO529_M_23_Liver_GT19-33750


title: DO525_M_23_Liver_GT19-33485


title: DO528_M_23_Liver_GT19-33558


title: DO527_M_23_Liver_GT19_33337


title: DO524_M_23_Liver_GT19_33360


title: DO546_M_23_Liver_GT19_33603


title: DO522_M_23_Liver_GT19_33384


title: DO521_M_23_Liver_GT19-33707


title: bone marrow_untreatment_SLE_R3

source_name: bone marrow,untreatment,SLE,R3


title: DO520_M_23_Liver_GT19_33593


title: DO523_M_23_Liver_GT19_33604


title: DO518_M_23_Liver_GT19_33452


title: DO517_M_23_Liver_GT19_33413


title: DO516_M_23_Liver_GT19-33678


title: DO519_M_23_Liver_GT19_33382


title: DO515_M_23_Liver_GT19-33487


title: DO514_M_23_Liver_GT19_33336


title: DO526_M_23_Liver_GT19-33749


title: DO538_M_23_Liver_GT19_33303


title: DO513_M_23_Liver_GT19-33505


title: DO508_F_23_Liver_GT19-33493


title: DO510_F_23_Liver_GT19-33704


title: DO506_F_23_Liver_GT19-33536


title: DO501_F_23_Liver_GT19-33736


title: DO511_M_23_Liver_GT19_33346


title: DO507_F_23_Liver_GT19-33497


title: DO504_F_23_Liver_GT19_33276


title: DO512_M_23_Liver_GT19-33539


title: DO500_F_23_Liver_GT19-33491


title: DO505_F_23_Liver_GT19-33468


title: DO503_F_23_Liver_GT19_33330


title: DO502_F_23_Liver_GT19_33398


title: DO498_F_23_Liver_GT19-33531


title: DO499_F_23_Liver_GT19_33605


title: DO497_F_23_Liver_GT19_33396


title: DO496_F_23_Liver_GT19_33300


title: DO494_F_23_Liver_GT19-33683


title: DO495_F_23_Liver_GT19_33388


title: DO489_F_23_Liver_GT19_33580


title: DO493_F_23_Liver_GT19-33463


title: DO488_F_23_Liver_GT19-33730


title: DO490_F_23_Liver_GT19_33621


title: DO492_F_23_Liver_GT19_33571


title: DO491_F_23_Liver_GT19_33422


title: DO487_F_23_Liver_GT19_33294


title: DO486_F_23_Liver_GT19-33691


title: DO485_F_23_Liver_GT19_33327


title: DO483_F_23_Liver_GT19_33378


title: DO482_F_23_Liver_GT19-33624


title: DO484_F_23_Liver_GT19_33306


title: DO478_F_23_Liver_GT19_33376


title: DO479_F_23_Liver_GT19_33606


title: DO480_F_23_Liver_GT19_33334


title: DO476_F_23_Liver_GT19_33371


title: DO472_F_23_Liver_GT19-33724


title: DO469_F_23_Liver_GT19_33363


title: DO474_F_23_Liver_GT19-33636


title: DO473_F_23_Liver_GT19-33684


title: DO468_F_23_Liver_GT19_33348


title: DO467_F_23_Liver_GT19_33280


title: DO477_F_23_Liver_GT19_33573


title: DO471_F_23_Liver_GT19-33706


title: DO466_F_23_Liver_GT19-33542


title: DO463_F_23_Liver_GT19-33654


title: DO465_F_23_Liver_GT19-33540


title: DO464_F_23_Liver_GT19_33290


title: DO417_M_21_Liver_GT19_33298


title: DO462_F_23_Liver_GT19-33649


title: DO415_M_21_Liver_GT19_33581


title: DO461_F_23_Liver_GT19-33526


title: DO420_M_21_Liver_GT19_33433


title: DO416_M_21_Liver_GT19-33745


title: DO414_M_21_Liver_GT19-33632


title: DO481_F_23_Liver_GT19_33435


title: DO411_M_21_Liver_GT19-33744


title: DO410_M_21_Liver_GT19_33325


title: DO475_F_23_Liver_GT19_33610


title: DO412_M_21_Liver_GT19-33731


title: DO470_F_23_Liver_GT19_33383


title: DO413_M_21_Liver_GT19_33421


title: DO409_M_21_Liver_GT19_33602


title: DO407_M_21_Liver_GT19_33286


title: DO405_M_21_Liver_GT19_33401


title: DO408_M_21_Liver_GT19_33598


title: DO404_M_21_Liver_GT19_33607


title: DO401_M_21_Liver_GT19-33648


title: DO403_M_21_Liver_GT19-33713


title: DO402_M_21_Liver_GT19_33560


title: DO406_M_21_Liver_GT19-33680


title: DO400_M_21_Liver_GT19_33596


title: DO399_M_21_Liver_GT19_33590


title: DO398_M_21_Liver_GT19_33595


title: DO380_M_21_Liver_GT19_33365


title: DO384_M_21_Liver_GT19_33361


title: DO379_M_21_Liver_GT19-33550


title: DO393_M_21_Liver_GT19-33642


title: DO396_M_21_Liver_GT19_33342


title: DO394_M_21_Liver_GT19_33313


title: DO382_M_21_Liver_GT19_33389


title: DO389_M_21_Liver_GT19_33279


title: DO383_M_21_Liver_GT19_33324


title: DO387_M_21_Liver_GT19_33420


title: DO397_M_21_Liver_GT19_33319


title: DO395_M_21_Liver_GT19-33503


title: DO385_M_21_Liver_GT19_33415


title: DO392_M_21_Liver_GT19-33637


title: DO381_M_21_Liver_GT19-33708


title: DO390_M_21_Liver_GT19-33517


title: DO386_M_21_Liver_GT19_33272


title: DO374_M_21_Liver_GT19-33740


title: DO373_M_21_Liver_GT19_33368


title: DO372_M_21_Liver_GT19-33549


title: DO371_M_21_Liver_GT19_33612


title: DO377_M_21_Liver_GT19_33292


title: DO388_M_21_Liver_GT19_33275


title: DO366_F_21_Liver_GT19_33601


title: DO370_F_21_Liver_GT19-33478


title: DO367_F_21_Liver_GT19_33369


title: DO369_F_21_Liver_GT19_33562


title: DO378_M_21_Liver_GT19-33679


title: DO376_M_21_Liver_GT19_33407


title: DO365_F_21_Liver_GT19-33700


title: DO357_F_21_Liver_GT19-33674


title: DO356_F_21_Liver_GT19-33675


title: DO361_F_21_Liver_GT19-33647


title: DO360_F_21_Liver_GT19_33395


title: DO364_F_21_Liver_GT19_33385


title: DO359_F_21_Liver_GT19_33462


title: DO354_F_21_Liver_GT19_33326


title: DO346_F_21_Liver_GT19_33308


title: DO343_F_21_Liver_GT19_33592


title: DO368_F_21_Liver_GT19-33464


title: DO345_F_21_Liver_GT19-33525


title: DO350_F_21_Liver_GT19_33425


title: DO347_F_21_Liver_GT19-33514


title: DO355_F_21_Liver_GT19_33594


title: DO352_F_21_Liver_GT19_33289


title: DO362_F_21_Liver_GT19-33474


title: DO353_F_21_Liver_GT19-33652


title: DO337_F_21_Liver_GT19_33574


title: DO338_F_21_Liver_GT19_33587


title: DO339_F_21_Liver_GT19_33318


title: DO342_F_21_Liver_GT19-33716


title: DO336_F_21_Liver_GT19_33339


title: DO358_F_21_Liver_GT19_33274


title: DO335_F_21_Liver_GT19-33748


title: DO348_F_21_Liver_GT19_33622


title: DO363_F_21_Liver_GT19-33737


title: DO349_F_21_Liver_GT19_33372


title: DO333_F_21_Liver_GT19_33450


title: DO344_F_21_Liver_GT19-33638


title: DO332_F_21_Liver_GT19_33620


title: DO330_F_21_Liver_GT19-33666


title: DO327_F_21_Liver_GT19-33646


title: DO328_F_21_Liver_GT19_33566


title: DO329_F_21_Liver_GT19_33442


title: DO326_F_21_Liver_GT19_33569


title: DO321_F_21_Liver_GT19_33316


title: DO322_F_21_Liver_GT19-33651


title: DO340_F_21_Liver_GT19-33538


title: DO319_M_19_Liver_GT19-33669


title: DO316_M_19_Liver_GT19-33469


title: DO315_M_19_Liver_GT19_33291


title: DO314_M_19_Liver_GT19_33340


title: DO312_M_19_Liver_GT19_33455


title: DO323_F_21_Liver_GT19-33695


title: DO325_F_21_Liver_GT19-33717


title: DO320_M_19_Liver_GT19_33577


title: DO311_M_19_Liver_GT19_33446


title: DO309_M_19_Liver_GT19-33511


title: DO331_F_21_Liver_GT19_33410


title: DO305_M_19_Liver_GT19-33489


title: DO313_M_19_Liver_GT19-33727


title: DO304_M_19_Liver_GT19_33404


title: DO324_F_21_Liver_GT19_33412


title: DO302_M_19_Liver_GT19-33524


title: DO318_M_19_Liver_GT19-33741


title: DO299_M_19_Liver_GT19_33406


title: DO308_M_19_Liver_GT19_33609


title: DO317_M_19_Liver_GT19_33399


title: DO296_M_19_Liver_GT19-33484


title: DO297_M_19_Liver_GT19_33354


title: DO301_M_19_Liver_GT19-33658


title: DO307_M_19_Liver_GT19_33293


title: DO293_M_19_Liver_GT19-33701


title: DO291_M_19_Liver_GT19-33481


title: DO292_M_19_Liver_GT19-33685


title: DO290_M_19_Liver_GT19_33564


title: DO303_M_19_Liver_GT19_33438


title: DO294_M_19_Liver_GT19-33518


title: DO295_M_19_Liver_GT19-33733


title: DO287_M_19_Liver_GT19_33567


title: DO288_M_19_Liver_GT19_33355


title: DO286_M_19_Liver_GT19_33441


title: DO285_M_19_Liver_GT19_33379


title: DO284_M_19_Liver_GT19-33671


title: DO281_M_19_Liver_GT19-33721


title: DO283_M_19_Liver_GT19-33483


title: DO282_M_19_Liver_GT19_33328


title: DO298_M_19_Liver_GT19_33288


title: DO280_M_19_Liver_GT19_33402


title: DO278_M_19_Liver_GT19_33583


title: DO279_M_19_Liver_GT19_33359


title: DO275_M_19_Liver_GT19_33305


title: DO277_M_19_Liver_GT19-33625


title: DO276_M_19_Liver_GT19-33639


title: DO274_M_19_Liver_GT19-33726


title: DO289_M_19_Liver_GT19-33555


title: DO273_M_19_Liver_GT19-33471


title: DO271_M_19_Liver_GT19_33615


title: DO269_F_19_Liver_GT19_33345


title: DO272_M_19_Liver_GT19_33409


title: DO260_F_19_Liver_GT19-33732


title: DO268_F_19_Liver_GT19-33547


title: DO267_F_19_Liver_GT19_33343


title: DO264_F_19_Liver_GT19-33528


title: DO262_F_19_Liver_GT19-33718


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title: DO320_M_19_GT20_00549_skeletal muscle


title: DO318_M_19_GT20_00456_skeletal muscle


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title: DO315_M_19_GT20_00221_skeletal muscle


title: DO321_F_21_GT20_00540_skeletal muscle


title: DO319_M_19_GT20_00473_skeletal muscle


title: DO312_M_19_GT20_00445_skeletal muscle


title: DO313_M_19_GT20_00489_skeletal muscle


title: DO314_M_19_GT20_00276_skeletal muscle


title: DO310_M_19_GT20_00355_skeletal muscle


title: DO309_M_19_GT20_00438_skeletal muscle


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title: DO303_M_19_GT20_00253_skeletal muscle


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title: DO299_M_19_GT20_00400_skeletal muscle


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title: DO296_M_19_GT20_00392_skeletal muscle


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title: DO294_M_19_GT20_00530_skeletal muscle


title: DO293_M_19_GT20_00499_skeletal muscle


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title: DO253_F_19_GT20_00300_skeletal muscle


title: DO256_F_19_GT20_00343_skeletal muscle


title: DO252_F_19_GT20_00427_skeletal muscle


title: DO254_F_19_GT20_00285_skeletal muscle


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title: DO175_M_18_GT20_00441_skeletal muscle


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title: DO174_M_18_GT20_00376_skeletal muscle


title: DO172_M_18_GT20_00341_skeletal muscle


title: DO169_F_18_GT20_00265_skeletal muscle


title: DO170_F_18_GT20_00498_skeletal muscle


title: DO173_M_18_GT20_00474_skeletal muscle


title: DO168_F_18_GT20_00678_skeletal muscle


title: DO166_F_18_GT20_00512_skeletal muscle


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title: DO160_F_18_GT20_00483_skeletal muscle


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title: DO155_F_18_GT20_00544_skeletal muscle


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title: DO052_F_17_GT20_00406_skeletal muscle


title: DO057_F_17_GT20_00611_skeletal muscle


title: DO072_M_17_GT20_00227_skeletal muscle


title: DO051_F_17_GT20_00274_skeletal muscle


title: DO050_F_17_GT20_00358_skeletal muscle


title: DO047_F_17_GT20_00409_skeletal muscle


title: DO048_F_17_GT20_00626_skeletal muscle


title: DO049_F_17_GT20_00354_skeletal muscle


title: DO046_F_17_GT20_00257_skeletal muscle


title: DO044_F_17_GT20_00418_skeletal muscle


title: DO043_F_17_GT20_00655_skeletal muscle


title: DO042_F_17_GT20_00347_skeletal muscle


title: DO039_F_17_GT20_00543_skeletal muscle


title: DO038_F_17_GT20_00533_skeletal muscle


title: DO040_F_17_GT20_00397_skeletal muscle


title: DO041_F_17_GT20_00547_skeletal muscle


title: DO037_F_17_GT20_00630_skeletal muscle


title: DO035_F_17_GT20_00684_skeletal muscle


title: DO036_F_17_GT20_00612_skeletal muscle


title: DO031_F_17_GT20_00417_skeletal muscle


title: DO033_F_17_GT20_00256_skeletal muscle


title: DO055_F_17_GT20_00698_skeletal muscle


title: DO032_F_17_GT20_00538_skeletal muscle


title: DO034_F_17_GT20_00369_skeletal muscle


title: DO028_F_17_GT20_00638_skeletal muscle


title: DO026_F_17_GT20_00407_skeletal muscle


title: DO025_F_17_GT20_00592_skeletal muscle


title: DO027_F_17_GT20_00670_skeletal muscle


title: DO024_F_17_GT20_00649_skeletal muscle


title: DO030_F_17_GT20_00238_skeletal muscle


title: DO054_F_17_GT20_00679_skeletal muscle


title: DO022_F_17_GT20_00475_skeletal muscle


title: DO021_F_17_GT20_00377_skeletal muscle


title: DO552_GT20_00335_adipose

data_processing:
Assembly: GRCm38
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.  counts_matrix.csv: raw counts quantified by EMASE and processed by/RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.  vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.  mrna_annots.csv: gene annotation file ENSEMBL version 75.
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

source_name: adipose

value: adipose

value: 45 percent  fat


title: DO554_GT20_00309_adipose


title: DO553_GT20_00431_adipose


title: DO549_GT20_00623_adipose


title: DO550_GT20_00219_adipose


title: DO548_GT20_00535_adipose


title: DO556_GT20_00316_adipose


title: DO558_GT20_00610_adipose


title: DO551_GT20_00683_adipose


title: DO560_GT20_00346_adipose


title: DO557_GT20_00615_adipose


title: DO555_GT20_00692_adipose


title: DO544_GT20_00327_adipose


title: DO547_GT20_00525_adipose


title: DO545_GT20_00413_adipose


title: DO542_GT20_00487_adipose


title: DO546_GT20_00607_adipose


title: DO543_GT20_00279_adipose


title: DO541_GT20_00598_adipose


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title: DO538_GT20_00541_adipose


title: DO536_GT20_00255_adipose


title: DO535_GT20_00240_adipose


title: DO534_GT20_00542_adipose


title: DO559_GT20_00356_adipose


title: DO531_GT20_00608_adipose


title: DO023_F_17_GT20_00504_skeletal muscle


title: DO533_GT20_00367_adipose


title: DO530_GT20_00482_adipose


title: DO529_GT20_00590_adipose


title: DO524_GT20_00651_adipose


title: DO523_GT20_00643_adipose


title: DO519_GT20_00606_adipose


title: DO528_GT20_00577_adipose


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title: DO511_GT20_00658_adipose


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title: DO518_GT20_00428_adipose


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title: DO506_GT20_00425_adipose


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title: DO512_GT20_00468_adipose


title: DO496_GT20_00604_adipose


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title: DO492_GT20_00701_adipose


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title: DO489_GT20_00537_adipose


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title: DO488_GT20_00313_adipose


title: DO482_GT20_00572_adipose


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title: DO484_GT20_00371_adipose


title: DO474_GT20_00339_adipose


title: DO480_GT20_00452_adipose


title: DO468_GT20_00588_adipose


title: DO472_GT20_00436_adipose


title: DO471_GT20_00666_adipose


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title: DO469_GT20_00269_adipose


title: DO477_GT20_00616_adipose


title: DO467_GT20_00322_adipose


title: DO476_GT20_00234_adipose


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title: DO465_GT20_00506_adipose


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title: DO473_GT20_00319_adipose


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title: DO410_GT20_00624_adipose


title: DO411_GT20_00617_adipose


title: DO409_GT20_00531_adipose


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title: DO398_GT20_00480_adipose


title: DO406_GT20_00621_adipose


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title: DO394_GT20_00249_adipose


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title: DO397_GT20_00645_adipose


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title: DO375_GT20_00471_adipose


title: DO369_GT20_00582_adipose


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title: DO370_GT20_00460_adipose


title: DO364_GT20_00567_adipose


title: DO363_GT20_00398_adipose


title: DO367_GT20_00495_adipose


title: DO360_GT20_00336_adipose


title: DO368_GT20_00352_adipose


title: DO359_GT20_00682_adipose


title: DO365_GT20_00462_adipose


title: DO357_GT20_00333_adipose


title: DO362_GT20_00591_adipose


title: DO361_GT20_00379_adipose


title: DO355_GT20_00554_adipose


title: DO356_GT20_00430_adipose


title: DO354_GT20_00514_adipose


title: DO353_GT20_00510_adipose


title: DO350_GT20_00307_adipose


title: DO352_GT20_00570_adipose


title: DO377_GT20_00348_adipose


title: DO349_GT20_00656_adipose


title: DO348_GT20_00283_adipose


title: DO366_GT20_00251_adipose


title: DO358_GT20_00326_adipose


title: DO347_GT20_00520_adipose


title: DO346_GT20_00349_adipose


title: DO344_GT20_00601_adipose


title: DO378_GT20_00509_adipose


title: DO343_GT20_00519_adipose


title: DO342_GT20_00412_adipose


title: DO345_GT20_00526_adipose


title: DO340_GT20_00639_adipose


title: DO338_GT20_00502_adipose


title: DO337_GT20_00437_adipose


title: DO336_GT20_00368_adipose


title: DO332_GT20_00580_adipose


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title: DO329_GT20_00493_adipose


title: DO335_GT20_00235_adipose


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title: DO318_GT20_00456_adipose


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title: DO333_GT20_00642_adipose


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title: DO307_GT20_00581_adipose


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title: DO306_GT20_00672_adipose


title: DO326_GT20_00308_adipose


title: DO304_GT20_00464_adipose


title: DO303_GT20_00253_adipose


title: DO302_GT20_00673_adipose


title: DO301_GT20_00384_adipose


title: DO299_GT20_00400_adipose


title: DO297_GT20_00685_adipose


title: DO323_GT20_00546_adipose


title: DO296_GT20_00392_adipose


title: DO295_GT20_00593_adipose


title: DO315_GT20_00221_adipose


title: DO294_GT20_00530_adipose


title: DO290_GT20_00518_adipose


title: DO312_GT20_00445_adipose


title: DO292_GT20_00363_adipose


title: DO291_GT20_00676_adipose


title: DO289_GT20_00292_adipose


title: DO288_GT20_00305_adipose


title: DO287_GT20_00289_adipose


title: DO286_GT20_00403_adipose


title: DO308_GT20_00627_adipose


title: DO285_GT20_00459_adipose


title: DO284_GT20_00426_adipose


title: DO300_GT20_00688_adipose


title: DO280_GT20_00448_adipose


title: DO282_GT20_00550_adipose


title: DO309_GT20_00438_adipose


title: DO279_GT20_00378_adipose


title: DO298_GT20_00560_adipose


title: DO275_GT20_00402_adipose


title: DO278_GT20_00224_adipose


title: DO274_GT20_00302_adipose


title: DO273_GT20_00558_adipose


title: DO293_GT20_00499_adipose


title: DO283_GT20_00408_adipose


title: DO272_GT20_00628_adipose


title: DO269_GT20_00282_adipose


title: DO265_GT20_00458_adipose


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title: Wildtype library 1

city: Stanford

first: Hunter

middle: B.

last: Fraser

state: California

address: 371 Jane Stanford Way

institute: Stanford University

data_processing:
All fastq files were aligned to the mouse (GRCm39, from ENSEMBL v109), rat (mRatBN7.2, from ENSEMBL v109), and a concatenated mouse and rat genome using CellRanger v7.1.048. For mapping, we retained protein-coding genes, lncRNA, antisense transcripts, snoRNA, snRNA, miRNA, and scaRNA. The resulting count matrices were read into scanpy and the proportion of aligned reads to each genome in the concatenated genome was used to determine the species of origin of each cell. A cell was assigned to mouse if greater than or equal to 70% of aligned reads aligned to the mouse genome, assigned to rat if greater than or equal to 70% of aligned reads aligned to the rat genome, and discarded as a doublet otherwise. For all subsequent steps, we only used the mouse-aligned-only counts for mouse cells and the rat-aligned-only counts for rat cells. We then removed all genes on sex chromosomes, restricted to mouse-rat one-to-one orthologs (defined using data from ENSEMBL), and performed standard pre-processing steps to remove low quality cells. For the latter, we performed standard filtering and removed cells with greater than 15% of counts coming from mitochondrial reads and cells with n_genes_by_counts (a commonly used quality control metric) greater than 7500. Next, we converted to the log normalized counts, identified highly variable genes, computed principal components, used the Python implementation of harmony to integrate the mouse and rat cells, and then found nearest neighbors. We then clustered the cells using the Leiden algorithm with resolution equal to 0.151. This first round of clustering split cells into neuronal, connective tissue, and hematopoietic lineages and then subsequent subclustering was done (see manuscript for details).
Assembly: mouse (GRCm39, from ENSEMBL v109), rat (mRatBN7.2, from ENSEMBL v109)
Supplementary files format and content: H5ad files were generated with Scanpy.  All_Cells_Start.h5ad contains the raw counts from all the cells that passed quality control.  Central_Nervous_System_Subclustered.h5ad contains normalized counts (see preprint for normalization details) and cell type information for central nervous system cell types.  GABAergic_Forebrain.h5ad contains normalized counts and cell type information for forebrain GABAergic lineage cells from Central_Nervous_System_Subclustered.h5ad that were further subclustered.  Chondrocyte_Subclustered.h5ad contains normalized counts and cell type information for chondrocyte lineage subtypes.  Mesenchymal_Subclustered.h5ad contains normalized counts and cell type information for chondrocyte lineage subtypes.

organism: Mus musculus x Rattus norvegicus

source_name: Connective tissue, forebrain, cord blood

growth_protocol: In brief, morula-stage embryos were obtained by uterus perfusion from superovulated CD1 mice at 2.5 days postcoitum (dpc). Morula-stage embryos were cultured in KSOM-AA medium (CytoSpring, Mountain View, CA; K0101) for 1 day and developed to blastocyst-stage embryos. Wild-type rat blastocysts were obtained by uterus perfusion from female rats at 4.5 dpc and cultured in Rat KSOM medium. For micromanipulation, mouse or rat ESCs were trypsinized and suspended in mouse or rat ESC culture medium. A piezo-driven micromanipulator (Prime Tech, Tsuchiura, Japan) was used to pierce the zona pellucida and trophectoderm under microscopy and 5–7 mouse or rat ESCs were introduced into blastocyst cavities near the inner cell mass. After blastocyst injection, embryos were cultured for 1–2 hours. Mouse blastocysts were then transferred into uteri of pseudopregnant recipient CD1 female mice at 2.5 dpc. Rat blastocysts were then transferred into uteri of pseudopregnant recipient Wistar female rats at 3.5 dpc. Table S1 shows results of the cell injection.

extract_protocol: Library preparation was done using the 10x v3.1 3' library preparation kit according to the manufacturer's instructions

treatment_protocol: Embryonic day (E) 15.25 mouse-rat and E13.5 rat-mouse chimeras were dissected to harvest forebrain and connective tissue. In brief, chimeric fetuses were collected from either E15.25 rat or E13.5 mouse pregnant mothers and forebrain and connective tissues were harvested from those chimeric fetuses. Both forebrains and connective tissues were dissociated in the solution containing 2mg/ml Collagenase/Dispase (Roche, Basel, Switzerland; 10269638001) in Hanks' Balanced Salt solution. After 30-60 min incubation at 37 degrees, 10% fetal bovine serum (FBS) in PBS solution was added into the tissue solution to inactivate the enzymes. All the dissociated cells were then filtered and used for the subsequent experiment. Dissociated cells derived from forebrain and connective tissue were stained with APC-anti-mouse CD45 antibody (Biolegend, San Diego, CA; 103112), PE-Cy7-anti rat CD45 (Biolegend: 202214). Donor chimerism was analyzed by detecting CD45 negative, tdTomato or GFP-expressing cells (detailed in Table S2). Both donor and host cells in the forebrain and connective tissue of chimeric fetuses were sorted using a FACS Aria II (BD, Franklin Lakes, NJ).

tag: mouse strain

tag: rat strain

value: Wistar

value: Wildtype


title: DO281_GT20_00507_adipose


title: DO262_GT20_00242_adipose


title: DO276_GT20_00668_adipose


title: DO263_GT20_00281_adipose


title: Rat-Mouse library 2

value: Connective tissue, forebrain, cord blood

value: Rat TdT+ ESC


title: DO277_GT20_00298_adipose


title: Rat-Mouse library 3


title: Mouse-Rat library 3

value: Mouse TdT+ ESC


title: DO264_GT20_00351_adipose


title: DO260_GT20_00467_adipose


title: DO259_GT20_00383_adipose


title: Mouse-Rat library 1


title: Rat-Mouse library 1


title: DO271_GT20_00366_adipose


title: DO258_GT20_00600_adipose


title: Mouse-Rat library 2


title: DO261_GT20_00561_adipose


title: DO257_GT20_00395_adipose


title: DO256_GT20_00343_adipose


title: ChIP-Seq(Control)_CdnL_Caulobacter_crescentus_NA1000_ΔcdnL(M2-G)

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

institute: University of Geneva, Faculty of Medicine / CMU

data_processing:
Base calling: NextSeq Control Software 4.0.2.7, RTA 2.11.3, bcl2fastq2.17 v2.17.1.14
Read Quality: FastQC (Galaxy Version 0.74+galaxy0), FASTQ Trimmer (Galaxy Version 1.1.5)
Alignment: Bowtie2 (Galaxy Version 2.4.5+galaxy1)
Peak calling: MACS2 (Galaxy Version 2.2.7.1+galaxy0 , No broad regions option) relative to the ΔcdnL negative ChIP-seq control. The q-value (false discovery rate, FDR) cut-off for called peaks was 0.05.
ChIP-Seq profiles RPM normalized and annotation: SeqMonk Software v1.47.2 (Braham Bionformatics Institute)
Assembly: Caulobacter crescentus NA1000 (NC_011916.1)
Supplementary files format and content: The xlsx file reporting CdnL (WT and *DD mutant) ChIP-Seq RPM normalized profiles was generated by SeqMonk software. The sheet is organized in columns as follows: column 1: Start (bp); column 2: End (bp); column 3: Feature; column 4: Description; column 5: Feature Strand; column 6: Feature Type; columns 7 to 15: CdnL (WT and *DD mutant) plus controls ChIP-Seq profiles (normalized Read Per Million unit, RPM)

organism: Caulobacter vibrioides

growth_protocol: C. crescentus strains WT (EG865), ∆cdnL (EG1898) and CdnLDD (EG2530) were grown overnight in 6 ml M2G (M2 with 0.2% glucose w/v) at 30°C (shaking at 200 rpm), respectively. The next day, cultures were diluted into 100 mL M2G and grown to an OD660nm of 0.5.

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, the cell resuspensions were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor Pico) at 4°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3–0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 ml using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of Protein-A agarose (Roche, www.roche.com) and 100 μg BSA. Five percent of the pre-cleared lysates were kept as total input samples. The rest of the pre-cleared lysates were then incubated overnight at 4°C with polyclonal rabbit antibodies targeting CdnL (1:1000 dilution). The Immuno-complexes were captured by incubation with Protein-A agarose beads (pre-saturated with BSA) during a 2 h incubation at 4°C and then, washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The immuno-complexes were eluted from the Protein-A beads with two times 250 μL elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like the total input sample, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 30 μl of DNAse/RNAse free water.
Immunoprecipitated chromatins were used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions. Single-end run was performed on an Illumina Next-Generation DNA sequencing instruments (NextSeq High), 50 cycles were performed and yielded several million reads per sequenced samples.

treatment_protocol: Cells were harvested (centrifugation at 8000 rpm during 10 min at 25°C) and, cell pellets were washed 3 times with 50 ml of M2 media (without glucose) at 25°C. Each of the washed cell pellets was split into two and used to inoculate 50 ml of M2 (carbon starvation) and 50 ml of M2G (preheated culture medium at 30°C), respectively. Cultures were incubated at 30⁰C (shaking at 200 rpm) for additional 60 minutes and then, supplemented with 10 μM sodium phosphate buffer (pH 7.6) and treated with formaldehyde (1% final concentration) at RT for 10 min to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 min on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were stored at -80°C.

tag: strain

value: delta-cdnL

tag: chip antibody

value: CdnL (polyclonal rabbit antibody)


title: Total-Input_CdnL_Caulobacter_crescentus_NA1000_ΔcdnL


title: ChIP-Seq(Control)_CdnL_Caulobacter_crescentus_NA1000_ΔcdnL(M2+G)


title: Total-Input_CdnL_Caulobacter_crescentus_NA1000_cdnLDD

value: cdnL-star-DD


title: DO254_GT20_00285_adipose


title: DO255_GT20_00244_adipose


title: DO253_GT20_00300_adipose


title: ChIP-Seq_CdnL_Caulobacter_crescentus_NA1000_cdnLDD(M2-G)


title: DO252_GT20_00427_adipose


title: ChIP-Seq_CdnL_Caulobacter_crescentus_NA1000_cdnLDD(M2+G)


title: Total-Input_CdnL_Caulobacter_crescentus_NA1000_WT

value: WT


title: ChIP-Seq_CdnL_Caulobacter_crescentus_NA1000_WT(M2+G)


title: DO251_GT20_00239_adipose


title: DO247_GT20_00433_adipose


title: DO245_GT20_00361_adipose


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title: DO242_GT20_00337_adipose


title: DO240_GT20_00527_adipose


title: DO238_GT20_00338_adipose


title: ChIP-Seq_CdnL_Caulobacter_crescentus_NA1000_WT(M2-G)


title: DO239_GT20_00686_adipose


title: DO237_GT20_00388_adipose


title: DO248_GT20_00444_adipose


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title: DO235_GT20_00690_adipose


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title: DO233_GT20_00301_adipose


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title: DO231_GT20_00674_adipose


title: DO230_GT20_00576_adipose


title: DO229_GT20_00589_adipose